Yeah, the examples in the OP weren't scary or anything but I could see how Majora's Mask had a foreboding feeling and uneasiness to it with the creepy moon's impending descension and some of the music in the game (Dead Hand in OOT was kinda creepy too, I guess). As far as in-game tension though, I'd say those damn E.M.M.I. robots in Dread were more terrifying than anything in Super Metroid. Still, Eternal Darkness trumps them all, obviously.

Never found the DKC games "dark" at all, other than the image brightness in some levels, lol.

Agreed with EMMI, those things were tense.  I always thought TP was one of Nintendo's darker themed games.  Especially the Ganon scene.

That's true.  I forgot about Twilight Princess, Ganon especially - much cooler than that frickin balloon-animal looking puppet in Wind Waker.

I mean obviously they're still E-rated games designed to be accessible to kids, I meant more that compared to their E-rated games today, the 90s had more of an "edge" to them where you occasionally got stuff that wasn't afraid to be a bit out there.

At the time I didn't think they were. It was just how things were with games in general. Was fairly common from every developer.

2000s Nintendo got pretty dark at times too. Super Paper Mario is rated E, and it is one of the darkest Mario games of all-time. Shoot it's darker than a lot of Nintendo games in general. TTYD had really dark moments, and even the original Paper Mario has Mario framed for murder.
Twilight Princess and Eternal Darkness go without saying but those are T and M.
And obviously Xenoblade gets really, really dark and it's in the 2010 onwards. But T rating once again.

Yeah at the time it wasn't unusual, it just strikes me how much things have changed when you compare it to E-rated games today.

This guy will forever have a free place to stay, free of rent, in my head:

Also, add an image of Zero-2 from Kirby 64 to that list in the opening post. Those dark moments that hit you the hardest are the ones that pop up in games that were never meant to be associated with horror or the macabre. 90s Nintendo was a master of that.

And thank you for adding the giant eel from Mario 64; everyone talks about the mad piano, but what about the huge ass eel with a mouth bigger than your entire body that drastically differs from the game's artistic aesthetics and looks like it could swallow you whole any time it wants to?

I'm glad you started this thread, because I was really wanting to continue the discussion on whether Nintendo will sanitize a potential Star Fox 64 remake that was in the OoT remake thread after the Star Fox direct turned speculation into reality.

In this post, I detailed how differently Andross was handled in Star Fox 0, a game that one can make the argument is a retelling/reimagining of Star Fox 64

https://gamrconnect.vgchartz.com/post.php?id=9651420

That's a great example of how Nintendo purposefully went in a direction to reduce the darker/scarier elements from old games. This new Star Fox is an even more direct, straight-up remake of Star Fox 64. I am highly interested in how it will handle all of its bosses, but the giant ape head and the brain with eyeballs especially. Lol, I'll have to watch a playthrough on YT to mentally prepare myself, kind of like how I have to use an arachnophobia guide to play Xenoblade.

I wonder in part if it was a clever way of working with the system's limitations at the time. A lot of PS1 games also had that dark look or used fog to hide the limited render distance, even something brighter like Driver did it. But then maybe it was liked so much, those limitations created their own art style that bled into popular culture where the need to do it wasn't necessary. As others said, movies and TV often had that look too, while popular music very much came from the outsiders of society, many were edgy and pushing what was socially acceptable in the 90s.

I grew up playing the GTA games on PS2 and the worlds felt massive at the time (GTA 3 is also very dark and Max Payne, while San Andreas used a lot of fog!) but then it became apparent from the remasters, how much the developers leaned into the hardware limitations to create that amazing atmosphere and a sense of depth often lacking in games nowadays. Limitations breed creativity.

As for Nintendo at the time, the one thing I really remember is the music and sound in their games really added to an amazing atmosphere that probably couldn't be replicated. Super Mario 64 was so echoey lol